Contacts of the helix formed by residues 153 - 160 (chain C) in PDB entry 1KXT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142C LYS* 6.0 0.9 - - - -
143C THR* 5.9 0.2 - - - +
150C SER* 3.7 3.2 + - - +
152C ASN* 1.3 79.2 - - - +
154C PRO* 1.3 61.4 - - - +
155C TYR* 2.9 30.8 + - - +
156C GLN* 3.4 43.0 + - - +
157C VAL* 2.7 30.0 - - - +
241C ALA* 4.7 0.4 - - - -
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Residues in contact with PRO 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ASN 3.7 8.3 - - - +
153C ASP* 1.3 89.8 - - - +
155C TYR* 1.3 73.4 + - + +
157C VAL* 3.7 3.0 + - + +
158C ARG* 3.1 52.8 + - - +
203C TRP* 4.5 3.1 - - + -
241C ALA* 3.7 19.3 - - + +
242C ILE* 3.7 14.4 - - + -
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Residues in contact with TYR 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LYS* 3.4 33.0 - - - +
153C ASP* 2.9 19.0 + - - +
154C PRO* 1.3 88.5 - - + +
156C GLN* 1.3 58.4 + - - +
158C ARG 3.4 1.0 + - - -
159C ASP* 2.9 39.7 + - - +
203C TRP* 3.7 33.1 - + - -
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Residues in contact with GLN 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LYS* 5.7 1.1 - - - +
143C THR* 3.5 21.1 - - + +
148C ILE* 3.6 4.9 - - + +
149C GLU* 2.7 34.0 + - - +
150C SER* 3.2 31.5 + - - +
153C ASP* 3.4 34.0 + - - +
155C TYR* 1.3 75.0 - - - +
157C VAL* 1.3 62.7 + - - +
158C ARG 2.8 11.8 + - - -
160C CYS* 2.8 50.9 + - + +
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Residues in contact with VAL 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ILE* 3.7 13.7 - - + +
150C SER 4.3 9.9 - - - +
151C TYR* 4.2 23.6 - - + -
153C ASP 2.7 26.7 - - - +
154C PRO* 3.9 4.9 - - + +
156C GLN* 1.3 74.6 - - - +
158C ARG* 1.3 63.2 + - + +
160C CYS 4.5 2.0 - - - +
200C LYS* 3.6 27.1 - - + +
201C HIS* 2.8 42.5 - - + +
242C ILE* 4.1 17.5 - - + -
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Residues in contact with ARG 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ASN* 4.2 2.3 + - - -
154C PRO* 3.1 25.9 + - - +
155C TYR 3.4 0.8 + - - +
156C GLN 2.8 2.6 + - - -
157C VAL* 1.3 79.4 - - + +
159C ASP* 1.3 54.4 + - - +
160C CYS 3.4 1.8 - - - -
167C ASP* 2.7 9.9 - - - +
200C LYS 3.7 5.1 + - - +
201C HIS 3.2 14.8 - - - +
202C MET* 3.2 22.4 + - - +
203C TRP* 3.3 60.4 + - + +
204C PRO* 3.9 10.3 - - - +
242C ILE* 3.1 35.0 - - - +
246C GLU* 3.2 20.0 + - - -
247C TYR* 3.2 19.4 + - - -
4003C CA 2.2 28.2 - - - -
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Residues in contact with ASP 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C ASN* 3.2 29.1 + - - +
140C LYS* 3.3 38.8 - - + +
141C CYS* 3.9 16.8 - - - +
142C LYS* 4.1 13.8 + - - -
155C TYR* 2.9 30.1 + - - +
158C ARG* 1.3 71.9 - - - +
160C CYS* 1.3 61.5 + - - +
161C GLN* 5.7 0.2 - - - +
167C ASP* 3.3 7.7 - - - +
203C TRP* 2.8 28.5 + - - -
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Residues in contact with CYS 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C CYS* 2.0 51.4 - - - -
142C LYS* 4.0 1.8 - - - -
143C THR* 3.9 5.8 - - - -
146C GLY 3.6 3.8 - - - +
147C GLY 3.8 13.0 - - - -
148C ILE* 4.0 5.2 - - - +
156C GLN* 2.8 43.1 + - - +
157C VAL 4.5 2.3 - - - +
158C ARG 4.3 2.6 - - - +
159C ASP* 1.3 79.9 - - - +
161C GLN* 1.3 65.2 + - - +
162C LEU* 3.7 1.9 + - - +
167C ASP* 3.5 16.8 - - - +
201C HIS* 5.6 1.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il